“core.kinematics.FoldTree” error upon running RAbD

This topic has 2 replies, 2 voices, and was last updated 5 years, 5 months ago by Anonymous.

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- June 27, 2020 at 12:27 am #3484
  Anonymous
  Dear all,
  
  I am trying to running RAbD with the following command:
  
  antibody_designer.linuxgccrelease
  
  -l design_input.list
  
  -primary_cdrs H3
  
  -graft_design_cdrs H3
  
  -seq_design_cdrs H1 H2
  
  -do_dock
  
  -paratope H3
  
  -mc_optimize_dG
  
  -mc_total_weight .001
  
  -mc_interface_weight .999
  
  -out:path:all designing
  
  -out:file:scorefile designing_scores.fasc
  
  -nstruct 3 | tee designing.log
  
  Strangely, the command sucessfully produce the some designed structures but I get the following error output information:
  
  core.kinematics.FoldTree: (1) [ FATAL ] FoldTree::edge_label(…) edge not in tree: 68 289
  
  What could be the possible reason and is it possible to correct it?
  
  Best regards!
- June 27, 2020 at 1:30 am #15359
  Anonymous
  Does your input structure have anything different with it? Any glycans, ligands, or post-translational modifications? Sometimes it’s that. If RAbD produced results, I wouldn’t worry about it too much. But if you have the full log, that would be helpful for me to debug it. It may just be Rosetta chatter, or a particular H3 that didn’t graft well.
- June 27, 2020 at 3:57 am #15360
  Anonymous
  The input structures have no glycans, ligands, or post-translational modifications. They are just models of ag-ab complexes built with Rosetta antibody and H3-modeling from the primary sequences and the Rosetta docking.protocol. It is possible that a particular H3 that didn’t graft well. But I hope that RAbD won’t stop just because there is a problem with only one input structure in the input list. The full log file can be found at:
  
  https://drive.google.com/file/d/18d6xmpJMD5NGHIlWnKS7muPnRztilwyB/view?usp=sharing
  
  Thanks!
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